PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme

Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is required. Although we have several techniques for the prediction of 4mC sites in different genomes based on both machine learning (ML) and convolutional neural networks (CNNs), there is no CNN-based tool for the identification of 4mC sites in the mouse genome. In this article, a CNN-based model named 4mCPred-CNN was developed to classify 4mC locations in the mouse genome. Until now, we had only two ML-based models for this purpose; they utilized several feature encoding schemes, and thus still had a lot of space available to improve the prediction accuracy. Utilizing only a single feature encoding scheme—one-hot encoding—we outperformed both of the previous ML-based techniques. In a ten-fold validation test, the proposed model, 4mCPred-CNN, achieved an accuracy of 85.71% and Matthews correlation coefficient (MCC) of 0.717. On an independent dataset, the achieved accuracy was 87.50% with an MCC value of 0.750. The attained results exhibit that the proposed model can be of great use for researchers in the fields of biology and bioinformatics.

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iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features

Bioinformatics ◽

10.1093/bioinformatics/btaa702 ◽

2020 ◽

Cited By ~ 1

Author(s):

Dan Zhang ◽

Zhao-Chun Xu ◽

Wei Su ◽

Yu-He Yang ◽

Hao Lv ◽

...

Keyword(s):

Protein Carbonylation ◽

Supplementary Information ◽

Sequence Information ◽

Biological Processes ◽

Feature Selection Technique ◽

Post Translational Modifications ◽

Proposed Model ◽

Feature Encoding ◽

Feature Encoding Scheme ◽

User Friendly

Abstract Motivation Protein carbonylation is one of the most important oxidative stress-induced post-translational modifications, which is generally characterized as stability, irreversibility and relative early formation. It plays a significant role in orchestrating various biological processes and has been already demonstrated to be related to many diseases. However, the experimental technologies for carbonylation sites identification are not only costly and time consuming, but also unable of processing a large number of proteins at a time. Thus, rapidly and effectively identifying carbonylation sites by computational methods will provide key clues for the analysis of occurrence and development of diseases. Results In this study, we developed a predictor called iCarPS to identify carbonylation sites based on sequence information. A novel feature encoding scheme called residues conical coordinates combined with their physicochemical properties was proposed to formulate carbonylated protein and non-carbonylated protein samples. To remove potential redundant features and improve the prediction performance, a feature selection technique was used. The accuracy and robustness of iCarPS were proved by experiments on training and independent datasets. Comparison with other published methods demonstrated that the proposed method is powerful and could provide powerful performance for carbonylation sites identification. Availability and implementation Based on the proposed model, a user-friendly webserver and a software package were constructed, which can be freely accessed at http://lin-group.cn/server/iCarPS. Supplementary information Supplementary data are available at Bioinformatics online.

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Study on laser-encoding scheme to antagonize active jamming abstract

Future Communication Technology ◽

10.2495/icct130581 ◽

2014 ◽

Author(s):

Qing-zhong Jia ◽

Yong-shan Liu ◽

Yan Ding

Keyword(s):

Encoding Scheme

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DeepSSPred: A Deep Learning Based Sulfenylation site predictor via a novel n-segmented optimize federated feature encoder

Protein and Peptide Letters ◽

10.2174/0929866527666201202103411 ◽

2020 ◽

Vol 27 ◽

Author(s):

Zaheer Ullah Khan ◽

Dechang Pi

Keyword(s):

Large Scale ◽

Computational Models ◽

Research Work ◽

Training Data ◽

Training Dataset ◽

Validation Dataset ◽

Cytokine Signaling ◽

Minority Class ◽

Independent Dataset ◽

Feature Encoding

Background: S-sulfenylation (S-sulphenylation, or sulfenic acid) proteins, are special kinds of post-translation modification, which plays an important role in various physiological and pathological processes such as cytokine signaling, transcriptional regulation, and apoptosis. Despite these aforementioned significances, and by complementing existing wet methods, several computational models have been developed for sulfenylation cysteine sites prediction. However, the performance of these models was not satisfactory due to inefficient feature schemes, severe imbalance issues, and lack of an intelligent learning engine. Objective: In this study, our motivation is to establish a strong and novel computational predictor for discrimination of sulfenylation and non-sulfenylation sites. Methods: In this study, we report an innovative bioinformatics feature encoding tool, named DeepSSPred, in which, resulting encoded features is obtained via n-segmented hybrid feature, and then the resampling technique called synthetic minority oversampling was employed to cope with the severe imbalance issue between SC-sites (minority class) and non-SC sites (majority class). State of the art 2DConvolutional Neural Network was employed over rigorous 10-fold jackknife cross-validation technique for model validation and authentication. Results: Following the proposed framework, with a strong discrete presentation of feature space, machine learning engine, and unbiased presentation of the underline training data yielded into an excellent model that outperforms with all existing established studies. The proposed approach is 6% higher in terms of MCC from the first best. On an independent dataset, the existing first best study failed to provide sufficient details. The model obtained an increase of 7.5% in accuracy, 1.22% in Sn, 12.91% in Sp and 13.12% in MCC on the training data and12.13% of ACC, 27.25% in Sn, 2.25% in Sp, and 30.37% in MCC on an independent dataset in comparison with 2nd best method. These empirical analyses show the superlative performance of the proposed model over both training and Independent dataset in comparison with existing literature studies. Conclusion : In this research, we have developed a novel sequence-based automated predictor for SC-sites, called DeepSSPred. The empirical simulations outcomes with a training dataset and independent validation dataset have revealed the efficacy of the proposed theoretical model. The good performance of DeepSSPred is due to several reasons, such as novel discriminative feature encoding schemes, SMOTE technique, and careful construction of the prediction model through the tuned 2D-CNN classifier. We believe that our research work will provide a potential insight into a further prediction of S-sulfenylation characteristics and functionalities. Thus, we hope that our developed predictor will significantly helpful for large scale discrimination of unknown SC-sites in particular and designing new pharmaceutical drugs in general.

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